The indictment alleges Keyes forced the teenager from the Common Grounds coffee stand in Anchorage on Feb. 1 and took her to his white pickup truck across the street, assistant U.S. Attorney Kevin Feldis said at a press conference.
Feldis said the suspect stole a debit card from a vehicle she shared that was parked near her home, obtained the personal identification number from Koenig and scratched the number into the card.
"The allegations continue that he confined her and intentionally killed her early the next morning after the abduction," he said.
Prosecutors said he flew back to Anchorage on about Feb. 17 and a week later, on Feb. 24, sent a text message using Koenig's phone. The message demanded ransom and directed that money could be deposited in the account connected to the stolen debit card.
Koenig's family followed the directions and deposited donated reward money into the account.
Police in Lufkin, Texas, stopped Keyes on March 11 on a speeding charge. He was quickly identified as a person of interest in the Koenig abduction.
Officers found rolls of cash bound in rubber bands and the stolen debit card, authorities said.
Keyes was then flown back to Anchorage and arraigned March 27 on the debit card fraud charge. A federal magistrate ordered him held without bail.
On April 2, divers pulled Koenig's body from the bottom of a frozen lake north of the city in the Matanuska-Susitna Borough.
The state of Alaska has no death penalty but Feldis said the crime of kidnapping and killing carries that potential under federal law. Feldis took no questions and did not address whether prosecutors will seek the death penalty. He also did not indicate how Koenig died.
Koenig's family said there was no apparent previous connection between the teen and the suspect.
"The investigation is continuing," said Anchorage Police Department spokesman Dave Parker. "This is just one step in the process."